A parametric simulation method for discrete dislocation dynamics

A new computer simulation method employed in discrete dislocation dynamics is presented. The article summarizes results of an application of the method to elementary interactions among glide dislocations and dipolar dislocation loops. The glide dislocations are represented by parametrically described curves moving in glide planes whereas the dipolar loops are treated as rigid objects. All mutual force interactions are considered in the models. As a consequence, the computational complexity rapidly increases with the number of objects considered. This difficulty is treated by advanced computational techniques such as suitable accurate numerical methods and parallel implementation of the algorithms. Therefore the method is able to simulate particular phenomena of dislocation dynamics which occur in crystalline solids deformed by single slip: generation of glide dislocations from the Frank-Read source, interaction of glide dislocations with obstacles, their encounters in channels of the bands, sweeping of dipolar loops by glide dislocations and a loop clustering.     

Electrochemically Gated Long‐Distance Charge Transport in Photosystem I

The transport of electrons along photosynthetic and respiratory chains involves a series of enzymatic reactions that are coupled through redox mediators, including proteins and small molecules. The use of native and synthetic redox probes is key to understanding charge transport mechanisms and to the design of bioelectronic sensors and solar energy conversion devices. However, redox probes have limited tunability to exchange charge at the desired electrochemical potentials (energy levels) and at different protein sites. Herein, we take advantage of electrochemical scanning tunneling microscopy (ECSTM) to control the Fermi level and nanometric position of the ECSTM probe in order to study electron transport in individual photosystem I (PSI) complexes. Current–distance measurements at different potentiostatic conditions indicate that PSI supports long‐distance transport that is electrochemically gated near the redox potential of P700, with current extending farther under hole injection conditions.     

Experimental analysis of contact for the indentation of a flat rounded punch

The ‘plane vs. plane’ contact involving flat punches has been the subject of many investigations, even in recent years, mainly due to the crucial role that such components play in phenomena, such as fretting fatigue and indentation tests. While the problem has been deeply approached from a theoretical point of view, there is a noteworthy lack of experimental verifications due to the limited number of laboratory techniques capable of supplying detailed information about contact parameters. In order to make a partial contribution towards gaining an understanding of such problems, this study proposes the investigation of flat rounded punch contact with an ultrasound-based technique, which exploits the properties of ultrasonic waves to be differently reflected by a contact interface depending on its stress state. A suitable setup was built in such a way as to ensure a good level of control of contact conditions, and the interface was scanned with a high-frequency ultrasonic transducer so as to acquire the reflection data. While the graphic processing of the ultrasonic coefficient of reflection may easily be displayed as a ‘contact map’, the quantitative accuracy of the method was also investigated by comparing experimental results with those obtained from a Finite Element model of the system. The results show a good level of agreement between the two approaches, thus confirming that the ultrasonic technique can be effectively employed to investigate many contact problems which to date have never (or scarcely) been experimentally validated.     

Highly populated turn conformations in natively unfolded tau protein identified from residual dipolar couplings and molecular simulation

Tau, a natively unstructured protein that regulates the organization of neuronal microtubules, is also found in high concentrations in neurofibrillary tangles of Alzheimer's disease and other neurodegenerative disorders. The conformational transition between these vastly different healthy and pathological forms remains poorly understood. We have measured residual dipolar couplings (RDCs), J-couplings, and nuclear Overhauser enhancement (NOE) in construct K18 of tau, containing all four repeat domains R1-R4. NHN RDCs were compared with prediction on the basis of a statistical model describing the intrinsic conformational sampling of unfolded proteins in solution. While local variation and relative amplitude of RDCs agrees with propensity-based prediction for most of the protein, homologous sequences in each repeat domain (DLKN, DLSN, DLSK, and DKFD in repeats R1-R4) show strong disagreement characterized by inversion of the sign of the central couplings. Accelerated molecular dynamic simulations (AMD) in explicit solvent revealed strong tendencies to form turns, identified as type I beta-turns for repeats R1-R3. Incorporation of the backbone dihedral sampling resulting from AMD into the statistical coil model closely reproduces experimental RDC values. These localized sequence-dependent conformational tendencies interrupt the propensity to sample more extended conformations in adjacent strands and are remarkably resistant to local environmental factors, as demonstrated by the persistence of the RDC signature even under harsh denaturing conditions (8 M urea). The role that this specific conformational behavior may play in the transition to the pathological form is discussed.     

Protein tyrosine phosphatase oligomerization studied by a combination of 15N NMR relaxation and 129Xe NMR. Effect of buffer containing arginine and glutamic acid

15N NMR relaxation and 129Xe NMR chemical shift measurements offer complementary information to study weak protein-protein interactions. They have been applied to study the oligomerization equilibrium of a low-molecular-weight protein tyrosine phosphatase in the presence of 50 mM arginine and 50 mM glutamic acid. These experimental conditions are shown to enhance specific protein-protein interactions while decreasing nonspecific aggregation. In addition, 129Xe NMR chemical shifts become selective reporters of one particular oligomer in the presence of arginine and glutamic acid, indicating that a specific Xe binding site is created in the oligomerization process. It is suggested that the multiple effects of arginine and glutamic acid are related to their effective excluded volume that favors specific protein association and the destabilization of partially unfolded forms that preferentially interact with xenon and are responsible for nonspecific protein aggregation.     

Optimizing sensitivity and resolution in time-shared NMR experiments

An improved approach to optimize the overall sensitivity and the resolution requirements in the indirect dimension of (13)C/(15)N time-shared (TS) NMR experiments is presented. A different data sampling acquisition procedure is applied for (13)C and (15)N in the indirect dimension, and a proper data recombination before conventional data processing allows a customized adjustment of spectral widths, number of scans and number of increments individually for (13)C and (15)N. The major benefit is an important improvement on the detection limits of the TS experiment that overcomes the lower sensitivity of (15)N over (13)C at natural abundance. We evaluate such enhancements from 2D TS-HMBC experiments recorded on a nitrogen-containing synthetic azole derivative of pharmaceutical interest.